1VFG

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog

Summary for 1VFG

• Entry DOI: 10.2210/pdb1vfg/pdb
• Related: 1MIW 1OU5 1R89 1UET
• Descriptor: RNA (75-MER), poly A polymerase, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, ... (4 entities in total)
• Functional Keywords: transferase, rna, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase-rna complex, transferase/rna
• Biological source: Aquifex aeolicus; More
• Total number of polymer chains: 4
• Total formula weight: 140764.80

Authors

Tomita, K.,Fukai, S.,Ishitani, R.,Ueda, T.,Takeuchi, N.,Vassylyev, D.G.,Nureki, O.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-04-13, release date: 2004-08-10, Last modification date: 2023-12-27)

Primary citation

Tomita, K.,Fukai, S.,Ishitani, R.,Ueda, T.,Takeuchi, N.,Vassylyev, D.G.,Nureki, O.
Structural basis for template-independent RNA polymerization.
Nature, 430:700-704, 2004

PubMed Abstract: The 3'-terminal CCA nucleotide sequence (positions 74-76) of transfer RNA is essential for amino acid attachment and interaction with the ribosome during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, 'CCA-adding enzyme', using CTP and ATP as substrates. Despite structural and biochemical studies, the mechanism by which the CCA-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. Here we present the crystal structure of Aquifex aeolicus CCA-adding enzyme, bound to a primer tRNA lacking the terminal adenosine and an incoming ATP analogue, at 2.8 A resolution. The enzyme enfolds the acceptor T helix of the tRNA molecule. In the catalytic pocket, C75 is adjacent to ATP, and their base moieties are stacked. The complementary pocket for recognizing C74-C75 of tRNA forms a 'protein template' for the penultimate two nucleotides, mimicking the nucleotide template used by template-dependent polymerases. These results are supported by systematic analyses of mutants. Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization.

PubMed: 15295603
DOI: 10.1038/nature02712

Experimental method

X-RAY DIFFRACTION (2.8 Å)